Email creations during AJO upgrade

We are experience lot of strange tings happening to out email when they are created during AJO updates. It seems to have some connection to our created email fragment that uses variables. Since it suddenly becomes problems with them, for a day or two. Then it goes back to normal. 

What happens is that fragments that uses variables, has a set av default values. In the templates where fragments is used and the default variables is changes to something else, they are reset to default in the templates they work on when the release is ongoing. 

This causes a lot of problems since out fragments has language and business areas values - when this changes it all becomes wrong. The logo changes to another business unit, and the footer becomes footer for another country and language. 

Can somebody confirm if our theory is correct, that a AJO release can effect emails that you are working on during the release.